POPSIM 2.13 – Population Simulation program

POPSIM 2.13

:: DESCRIPTION

POPSIM creates a virtual representation of every individual,makes no prior assumptions but the Medelian rules and allows for populations of several million individuals size to be generated and to be followed over hundreds of generations.

::DEVELOPER

Institute for Clinical Molecular Biology

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows

:: DOWNLOAD

 POPSIM

:: MORE INFORMATION

Citation

Hampe J, Wienker T, Schreiber S, Nürnberg T (1998).
POPSIM: A general population simulation program.
Bioinformatics 14: 458-464

varLD 1.0 – Comparison of Variation in Linkage Disequilibrium between Population

varLD 1.0

:: DESCRIPTION

varLD can be used to perform inter-population comparison of regional patterns of linkage disequilibrium (LD), and quantifies which genomic regions carry dissimilar patterns of LD across the populations compared.

::DEVELOPER

Saw Swee Hock School of Public Health

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsXR package
  • Java

:: DOWNLOAD

  varLD

:: MORE INFORMATION

Citation:

varLD: a program for quantifying variation in linkage disequilibrium patterns between populations.
Ong RT, Teo YY.
Bioinformatics. 2010 May 1;26(9):1269-70. doi: 10.1093/bioinformatics/btq125. Epub 2010 Mar 22.

WinXPCNVer – Calculating Vst values between two Populations Probe

WinXPCNVer

:: DESCRIPTION

WinXPCNVer is tool package for calculating the Vst values between two populations probe by probe in a sliding window, which could be used to detect highly differentiated variants between populations.

::DEVELOPER

Population Genomics Group (PGG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

WinXPCNVer

:: MORE INFORMATION

Citation

Lou H, Lu Y, Lu D, Fu R, Wang X, Feng Q, Wu S, Yang Y, Li S, Kang L, Guan Y, Hoh BP, Chung YJ, Jin L, Su B, Xu S.
A 3.4-kb Copy-Number Deletion near EPAS1 Is Significantly Enriched in High-Altitude Tibetans but Absent from the Denisovan Sequence.
Am J Hum Genet. 2015 Jul 2;97(1):54-66. doi: 10.1016/j.ajhg.2015.05.005. Epub 2015 Jun 11. PMID: 26073780; PMCID: PMC4572470.

AncestryPainter v5 – Illuminate the Ancestry Compositions of Populations and Individuals

AncestryPainter v5

:: DESCRIPTION

AncestryPainter is a graphic program used to illuminate the ancestry compositions of populations and individuals in a way to save space with a rounded and nice-looking graph.

::DEVELOPER

Population Genomics Group (PGG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • R

:: DOWNLOAD

AncestryPainter

:: MORE INFORMATION

Citation

Feng Q, Lu D, Xu S.
AncestryPainter: A Graphic Program for Displaying Ancestry Composition of Populations and Individuals.
Genomics Proteomics Bioinformatics. 2018 Oct;16(5):382-385. doi: 10.1016/j.gpb.2018.05.002. Epub 2018 Nov 22. PMID: 30472416; PMCID: PMC6364040.

AdmixSim 2.0 – Forward-time Simulator of Population Genetic data

AdmixSim 2.0

:: DESCRIPTION

AdmixSim is an individual-based forward-time simulation tool that can flexibly and efficiently simulate population genomics data under complex evolutionary scenarios. It is based on the extended Wright-Fisher model, and it implements many common evolutionary parameters to involve gene flow, natural selection, recombination, and mutation.

::DEVELOPER

Population Genomics Group (PGG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

AdmixSim

:: MORE INFORMATION

Citation

Zhang R, Liu C, Yuan K, Ni X, Pan Y, Xu S.
AdmixSim 2: a forward-time simulator for modeling complex population admixture.
BMC Bioinformatics. 2021 Oct 18;22(1):506. doi: 10.1186/s12859-021-04415-x. PMID: 34663213; PMCID: PMC8522168.

deepTS – Exploring Transcriptional Switches from pairwise, temporal, and population RNA-Seq data

deepTS

:: DESCRIPTION

deepTS is a powerful and flexible web-based Galaxy platform for identifying, visualizing and analyzing transcriptional switch (TS) events from pairwise, temporal and population transcriptome data.

::DEVELOPER

Ma Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

deepTS

:: MORE INFORMATION

Citation

Qiu Z, Chen S, Qi Y, Liu C, Zhai J, Xie S, Ma C.
Exploring transcriptional switches from pairwise, temporal and population RNA-Seq data using deepTS.
Brief Bioinform. 2021 May 20;22(3):bbaa137. doi: 10.1093/bib/bbaa137. PMID: 32728687.

HIPPO 1.0/ AEML 1.0 – Estimate Population Haplotype Frequencies from Pooled SNP data

HIPPO 1.0/ AEML 1.0

:: DESCRIPTION

Hippo (Haplotype estimation under incomplete prior information using pooled observations) is a program for estimating haplotype distribution from pooled DNA data and is able to utilize prior information about the haplotypes that are known to be present in the population.

AEML is a program for estimating haplotype distribution from pooled DNA data and is able to utilize prior information about the haplotypes that are known to be present in the population.

::DEVELOPER

Matti Pirinen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

  HIPPO  – AEML Source Code

:: MORE INFORMATION

Citation

Matti Pirinen
Estimating population haplotype frequencies from pooled SNP data using incomplete database information
Bioinformatics (2009) 25 (24): 3296-3302

AgeStructure 1.0 – Estimate Effective Size & Generation Interval of Population with overlapping Generations

AgeStructure 1.0

:: DESCRIPTION

AgeStructure is a computer program for estimating the generation interval, effective size, variances and covariances of lifetime number of offspring of an age structured population with overlapping generations.

:: DEVELOPER

Dr Jinliang Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Fortran 90/95 compiler

:: DOWNLOAD

 AgeStructure

:: MORE INFORMATION

Citation

Wang, J., Brekke, P. , Huchard, E., Knapp, L. A. , Cowlishaw, G. 2010.
Estimation of parameters of inbreeding and genetic drift in populations with overlapping generations.
Evolution, 64, 1704–1718.

bammds 2014 – Create MDS plot of Populations for Genetic data

bammds 2014

:: DESCRIPTION

bammds is a software that allows to create a multidimensional scaling (MDS) plot of populations for genetic data.

::DEVELOPER

bammds team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • samtools
  • R
  • Perl

:: DOWNLOAD

 bammds

:: MORE INFORMATION

Citation

bammds: A tool for assessing the ancestry of low depth whole genome data using multidimensional scaling (MDS).
Malaspinas AS, Tange O, Moreno-Mayar JV, Rasmussen M, DeGiorgio M, Wang Y, Valdiosera CE, Politis G, Willerslev E, Nielsen R.
Bioinformatics. 2014 Jun 28. pii: btu410.

VarB 1.4 – Population Genomic Variation Browser

VarB 1.4

:: DESCRIPTION

Varb is a variant display and analysis tool for VCF files. The basic inputs are a reference genome (fasta format), variants (VCF) and annotation (GFF format) files. In real-time, the software filters variants and updates calculated population genetic matrics

::DEVELOPER

PathogenSeq

:: SCREENSHOTS

VarB

:: REQUIREMENTS

  • Linux / Windows
  • QT

:: DOWNLOAD

 VarB

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2983-5. doi: 10.1093/bioinformatics/bts557. Epub 2012 Sep 13.
VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data.
Preston MD1, Manske M, Horner N, Assefa S, Campino S, Auburn S, Zongo I, Ouedraogo JB, Nosten F, Anderson T, Clark TG.